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Computational analysis and characterization of UCE-like elements (ULEs) in plant genomes


Kritsas, Konstantinos; Wuest, Samuel E; Hupalo, Daniel; Kern, Andrew D; Wicker, Thomas; Grossniklaus, Ueli (2012). Computational analysis and characterization of UCE-like elements (ULEs) in plant genomes. Genome Research, 22(12):2455-2466.

Abstract

Ultraconserved elements (UCEs), stretches of DNA that are identical between distantly related species, are enigmatic genomic features whose function is not well understood. First identified and characterized in mammals, UCEs have been proposed to play important roles in gene regulation, RNA processing, and maintaining genome integrity. However, because all of these functions can tolerate some sequence variation, their ultraconserved and ultraselected nature is not explained. We investigated whether there are highly conserved DNA elements without genic function in distantly related plant genomes. We compared the genomes of Arabidopsis thaliana and Vitis vinifera; species that diverged ∼115 million years ago (Mya). We identified 36 highly conserved elements with at least 85% similarity that are longer than 55 bp. Interestingly, these elements exhibit properties similar to mammalian UCEs, such that we named them UCE-like elements (ULEs). ULEs are located in intergenic or intronic regions and are depleted from segmental duplications. Like UCEs, ULEs are under strong purifying selection, suggesting a functional role for these elements. As their mammalian counterparts, ULEs show a sharp drop of A+T content at their borders and are enriched close to genes encoding transcription factors and genes involved in development, the latter showing preferential expression in undifferentiated tissues. By comparing the genomes of Brachypodium distachyon and Oryza sativa, species that diverged ∼50 Mya, we identified a different set of ULEs with similar properties in monocots. The identification of ULEs in plant genomes offers new opportunities to study their possible roles in genome function, integrity, and regulation.

Abstract

Ultraconserved elements (UCEs), stretches of DNA that are identical between distantly related species, are enigmatic genomic features whose function is not well understood. First identified and characterized in mammals, UCEs have been proposed to play important roles in gene regulation, RNA processing, and maintaining genome integrity. However, because all of these functions can tolerate some sequence variation, their ultraconserved and ultraselected nature is not explained. We investigated whether there are highly conserved DNA elements without genic function in distantly related plant genomes. We compared the genomes of Arabidopsis thaliana and Vitis vinifera; species that diverged ∼115 million years ago (Mya). We identified 36 highly conserved elements with at least 85% similarity that are longer than 55 bp. Interestingly, these elements exhibit properties similar to mammalian UCEs, such that we named them UCE-like elements (ULEs). ULEs are located in intergenic or intronic regions and are depleted from segmental duplications. Like UCEs, ULEs are under strong purifying selection, suggesting a functional role for these elements. As their mammalian counterparts, ULEs show a sharp drop of A+T content at their borders and are enriched close to genes encoding transcription factors and genes involved in development, the latter showing preferential expression in undifferentiated tissues. By comparing the genomes of Brachypodium distachyon and Oryza sativa, species that diverged ∼50 Mya, we identified a different set of ULEs with similar properties in monocots. The identification of ULEs in plant genomes offers new opportunities to study their possible roles in genome function, integrity, and regulation.

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12 citations in Scopus®
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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:07 Faculty of Science > Department of Plant and Microbial Biology
07 Faculty of Science > Zurich-Basel Plant Science Center
Dewey Decimal Classification:580 Plants (Botany)
Language:English
Date:2012
Deposited On:22 Feb 2013 14:59
Last Modified:05 Apr 2016 16:32
Publisher:Cold Spring Harbor Laboratory Press
ISSN:1088-9051
Free access at:Publisher DOI. An embargo period may apply.
Publisher DOI:https://doi.org/10.1101/gr.129346.111
PubMed ID:22987666

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